def test_batch_fastqs_multiple_fastqs_single_batch(self):
"""batch_fastqs: multiple Fastqs, single batch
"""
fqs = batch_fastqs([self.r1, self.r1, self.r1, self.r1],
batch_size=12,
out_dir=self.wd)
self.assertEqual(fqs, [
os.path.join(self.wd, "batched.B000.r1.fastq"),
])
for fq in fqs:
self.assertTrue(os.path.exists(fq))
tmpdir = os.path.abspath(args.temporary_directory)
else:
try:
tmpdir = os.path.abspath(os.environ["TMPDIR"])
except KeyError:
tmpdir = None
working_dir = tempfile.mkdtemp(suffix="icell8_stats", dir=tmpdir)
print "Using working dir %s" % working_dir
# Split into batches for multiprocessing
if nprocs > 1:
try:
batch_size, nbatches = get_batch_size(
fastqs, max_batch_size=args.max_batch_size, min_batches=nprocs)
batched_fastqs = batch_fastqs(fastqs,
batch_size,
basename="icell8_stats",
out_dir=working_dir)
except Exception as ex:
logging.critical("Failed to split Fastqs into batches: " "%s" % ex)
sys.exit(1)
else:
batched_fastqs = fastqs
# Collect statistics
stats = ICell8Stats(*batched_fastqs, nprocs=nprocs, verbose=True)
# Remove the working directory
shutil.rmtree(working_dir)
# Report the stats
if args.stats_file is not None: